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provides common tools and lookup tables used primarily by the hgvs and uta packages

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biocommons/bioutils

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bioutils -- bioinformatics utilities and lookup tables

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bioutils provides some common utilities and lookup tables for bioinformatics.

  • bioutils.accessions -- parse accessions, infer namespaces
  • bioutils.assemblies -- Human assembly information (from NCBI/GRCh)
  • bioutils.cytobands -- map cytobands to coordinates (from UCSC cytoband tables)
  • bioutils.digests -- implementations of various digests
  • bioutils.normalize -- allele normalization (left shuffle, right shuffle, expanded, vcf)

To use an E-Utilities API key run add it to an environment variable called ncbi_api_key and it will be used in the E-Utilities request.